How Does Intermittent Fasting Affect Gut Health?

Intermittent fasting can have a major impact on gut health. It has been linked to health benefits including the slowing or reversal of aging and disease processes and the improvement of overall physical and mental health. (1)

Fasting improves the intestinal microbiome by decreasing intestinal inflammation, increasing intestinal stem cells, and expanding the number of protective gut bacteria. (2-4, 5). A recently published controlled clinical study completed such an investigation and found changes in gut microbial makeup, longevity-related genes, and signaling proteins. (5)

The fasting group showed differences in gut microbial composition and an expansion of diversity at the phylum and species levels. (5) Researchers noted a significant increase for Christensenella. (5) This longevity-relevant gut microbiota has previously been associated with the gut microbial make-up of centenarians. (6) Also, the study results suggested that periodic fasting affects gene expression (SIRTs) in blood cells. (5) SIRTs are signaling proteins involved in metabolic function and cellular health, including DNA repair, cell survival, and stress resistance. Additionally, ketone body production was increased during the fasting treatment. Of interest, one of the ketone bodies, beta-hydroxybutyrate (BHB). BHB has been associated with cellular signaling, gene expression regulation, and the potential reduction of age-related neurological impairments. (5)

Results from this 2021 clinical study suggest that periodic fasting not only changes the composition of the intestinal microbiota, creating more diversity at the species level but also increases both SIRT expression and the expression of those genes and microbiota relevant to aging and longevity in humans. Fasting-related research continues to evolve, with a focus on therapeutic applications for addressing chronic disease and optimizing a patient’s health.

In Simple Terms: Why Does Intermittent Fasting Have So Many Benefits?

Being in a fasted state activates cellular pathways that remove or repair damaged molecules and improve our defense against oxidative and metabolic stress.
Evidence now indicates that intermittent fasting has several positive effects that are unrelated to weight, including:

  • Improving blood sugar regulation, heart rate, and blood pressure
  • Increasing stress resistance
  • Slowing the effects of aging
  • Reducing inflammation
  • Improving cognitive function

Nutrition and Fasting Interventions for Mitochondrial Health

Specific nutrients that support mitochondrial function may be part of a personalized nutrition strategy for some patients. In other cases, a form of intermittent fasting may be appropriate and blended with a food plan to create an individualized nutrition intervention. Several forms of intermittent fasting* include the following:

  • Alternate-day fasting: A cycle of fasting on one day and eating on the next day.
  • Time-restricted feeding: An approach that considers circadian rhythms and advocates consuming calories from food and beverages only during a shortened window of time daily, also called “prolonged nightly fasting,” which extends a person’s nightly fast to 12 hours or more.
  • Fasting-mimicking diet: A periodic, multiple-day, plant-based diet program low in calories, sugars, and protein but high in unsaturated fats with the inclusion of supplements for vitamins, minerals, and essential fatty acids.

All can be effective, but in my work with patients, I have found that time-restricted eating is the most practical and sustainable approach for most people.
There is some evidence that eating only in the morning or daytime is better than later in the day and evening.

If you would like to give time-restricted eating a try, make sure to start slowly to give your body a chance to adapt.

One Approach to Intermittent Fasting is the Functional Medicine Mitochondrial Food Plan. The food plan is an anti-inflammatory, low-glycemic, high-quality fat approach to eating that supports healthy mitochondria for improved energy production. Further, this food plan can be expanded with various levels of fasting.

Additionally, chronic conditions may already have elevated levels of inflammation and oxidative stress, and the current diet may need to be balanced to reduce overall inflammation before introducing fasting. Functional medicine provides personalized therapeutic strategies that potentially include nutrition interventions incorporating different levels of fasting.

If you think that this type of treatment might be right for you, then consider signing up for a free discovery call so we can answer any questions you may have.


  1. de Cabo R, Mattson MP. Effects of intermittent fasting on health, aging, and disease [published correction appears in N Engl J Med. 2020;382(3):298; N Engl J Med. 2020;382(10):978]. N Engl J Med. 2019;381(26):2541-2551. doi:10.1056/NEJMra1905136
  2. Cignarella F, Cantoni C, Ghezzi L, et al. Intermittent fasting confers protection in CNS autoimmunity by altering the gut microbiota. Cell Metab. 2018;27(6):1222-1235.e6. doi:10.1016/j.cmet.2018.05.006
  3. Rangan P, Choi I, Wei M, et al. Fasting-mimicking diet modulates microbiota and promotes intestinal regeneration to reduce inflammatory bowel disease pathology. Cell Rep. 2019;26(10):2704-2719.e6. doi:10.1016/j.celrep.2019.02.019
  4. Schmidt NS, Lorentz A. Dietary restrictions modulate the gut microbiota: implications for health and disease. Nutr Res. 2021;89:10-22. doi:10.1016/j.nutres.2021.03.001
  5. Lilja S, Stoll C, Krammer U, et al. Five days of periodic fasting elevates levels of longevity related Christensenellaand sirtuin expression in humans. Int J Mol Sci. 2021;22(5):2331. doi:10.3390/ijms22052331

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